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Hence proteomics data sets will contain at least a thousand fold less sequence information than genomic databases but have much more numerical data including m/z values and continuous intensity values from the parent and fragment ions [ 10, 11].
The mean and median CRR values were fairly consistent between the different assemblies, with the exception of TA_454 that had lower coverage per CCDS and therefore would provide less sequence information per transcript.
This analysis, based on less sequence information, also moved Nv85341 to the edge of the DD group, but the central conclusion of great diversity of thrombospondin sequences within N. vectensis is upheld.
These databases are less suitable for certain groups of organisms, such as protists and viruses, which are extremely diverse and for which considerably less sequence information is available compared to bacteria.
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Through a genome wide analysis, we selected 41 pairs of adjacent CNE located on various chromosomes in zebrafish and obtained their intervening, less conserved, sequence information from rainbow trout.
Because B-SIFT uses an amino acid substitution as input and interpretation of allele frequencies would be complicated by multi-allelic SNPs, only bi-allelic missense SNPs were used in this analysis, resulting in a set of 32261 nonsynonymous SNPs (22,219 with median sequence information less than or equal to 3.25).
*Clones for which sequence information was less than 200 nucleotides have not yet been submitted to Genbank.
The summary evaluation results in Table 3 show that the use of single sequence information provides less sensitivity but more specificity than the use of PSSM scoring.
On the other hand, the cDNA-AFLP technique has become one of the most robust solutions for differential display and it has been successfully applied in several quantitative gene expression studies [ 21, 24, 40, 61, 62], even in less investigated species for which sequence information is not available.
Mapping interaction interfaces using this type of information is less sequence specific than that with the chemical shift perturbations observed with PFI1780w, as loss of resonance intensity may reflect interactions by a specific residue or its neighbors.
This class of markers are particularly important for less studied species, for which genome sequence information is generally not known.
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